bmtk.utils package¶
Subpackages¶
- bmtk.utils.compile_mechanisms package
- bmtk.utils.create_environment package
- bmtk.utils.io package
- Submodules
- bmtk.utils.io.cell_vars module
CellVarRecorder
CellVarRecorder.DataTable
CellVarRecorder.add_cell()
CellVarRecorder.close()
CellVarRecorder.dt
CellVarRecorder.flush()
CellVarRecorder.initialize()
CellVarRecorder.is_initialized
CellVarRecorder.merge()
CellVarRecorder.record_cell()
CellVarRecorder.record_cell_block()
CellVarRecorder.tstart
CellVarRecorder.tstop
CellVarRecorderParallel
- bmtk.utils.io.firing_rates module
- bmtk.utils.io.ioutils module
- bmtk.utils.io.spike_trains module
- Module contents
- bmtk.utils.reports package
- Subpackages
- bmtk.utils.reports.compartment package
- bmtk.utils.reports.spike_trains package
- Submodules
- bmtk.utils.reports.spike_trains.core module
- bmtk.utils.reports.spike_trains.plotting module
- bmtk.utils.reports.spike_trains.spike_train_buffer module
- bmtk.utils.reports.spike_trains.spike_train_readers module
- bmtk.utils.reports.spike_trains.spike_trains module
- bmtk.utils.reports.spike_trains.spike_trains_api module
- bmtk.utils.reports.spike_trains.spikes_file_writers module
- bmtk.utils.reports.spike_trains.stats module
- Module contents
- Submodules
- bmtk.utils.reports.current_writer module
CurrentWriterv01
CurrentWriterv01.DataTable
CurrentWriterv01.close()
CurrentWriterv01.dt()
CurrentWriterv01.flush()
CurrentWriterv01.initialize()
CurrentWriterv01.merge()
CurrentWriterv01.n_steps()
CurrentWriterv01.record_clamps()
CurrentWriterv01.set_dt()
CurrentWriterv01.set_tstart()
CurrentWriterv01.set_tstop()
CurrentWriterv01.set_units()
CurrentWriterv01.tstart()
CurrentWriterv01.tstop()
CurrentWriterv01.units()
- Module contents
- Subpackages
- bmtk.utils.sonata package
- Subpackages
- Submodules
- bmtk.utils.sonata.column_property module
- bmtk.utils.sonata.edge module
- bmtk.utils.sonata.file module
- bmtk.utils.sonata.file_root module
- bmtk.utils.sonata.group module
- bmtk.utils.sonata.node module
- bmtk.utils.sonata.population module
EdgePopulation
EdgePopulation.build_indicies()
EdgePopulation.edge_types_table
EdgePopulation.filter()
EdgePopulation.get_row()
EdgePopulation.get_source()
EdgePopulation.get_source_population()
EdgePopulation.get_sources()
EdgePopulation.get_target()
EdgePopulation.get_target_population()
EdgePopulation.get_targets()
EdgePopulation.group_id_column
EdgePopulation.group_index_column
EdgePopulation.group_indicies()
EdgePopulation.next()
EdgePopulation.source_population
EdgePopulation.target_population
EdgePopulation.to_dataframe()
EdgePopulation.type_ids_column
NodePopulation
NodePopulation.add_gids()
NodePopulation.filter()
NodePopulation.get_gid()
NodePopulation.get_node_id()
NodePopulation.get_row()
NodePopulation.get_rows()
NodePopulation.gids
NodePopulation.group_id_column
NodePopulation.group_index_column
NodePopulation.has_gids
NodePopulation.igids()
NodePopulation.index_column_name
NodePopulation.inode_ids()
NodePopulation.inode_type_ids()
NodePopulation.next()
NodePopulation.node_ids
NodePopulation.node_types_table
NodePopulation.to_dataframe()
NodePopulation.type_ids_column
Population
Population.get_group()
Population.group_id_column
Population.group_id_ds
Population.group_ids
Population.group_index_column
Population.group_index_ds
Population.group_indicies()
Population.groups
Population.igroup_ids()
Population.igroup_indicies()
Population.name
Population.to_dataframe()
Population.type_ids
Population.type_ids_column
Population.types_table
- bmtk.utils.sonata.types_table module
- bmtk.utils.sonata.utils module
- Module contents
Submodules¶
bmtk.utils.hdf5_helper module¶
bmtk.utils.lazy_property module¶
bmtk.utils.sim_setup module¶
- class bmtk.utils.sim_setup.BioNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
EnvBuilder
- property bmtk_simulator¶
- property examples_dir¶
- property target_simulator¶
- class bmtk.utils.sim_setup.EnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
object
- property base_dir¶
- property bmtk_simulator¶
- build(include_examples=False, use_relative_paths=True, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, config_file='config.json', overwrite_config=False, **run_args)[source]¶
- property components_dir¶
- property examples_dir¶
- property network_dir¶
- property node_sets_file¶
- property output_dir¶
- property scripts_root¶
- property target_simulator¶
- class bmtk.utils.sim_setup.FilterNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
EnvBuilder
- property bmtk_simulator¶
- property examples_dir¶
- property target_simulator¶
- class bmtk.utils.sim_setup.PointNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
EnvBuilder
- property bmtk_simulator¶
- property examples_dir¶
- property target_simulator¶
- class bmtk.utils.sim_setup.PopNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
EnvBuilder
- property bmtk_simulator¶
- property examples_dir¶
- property target_simulator¶
- bmtk.utils.sim_setup.build_env_bionet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, overwrite_config=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=-15.0, nsteps_block=5000, v_init=-80.0, celsius=34.0, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, compile_mechanisms=False, use_relative_paths=True, config_file=None)[source]¶
- bmtk.utils.sim_setup.build_env_filternet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, config_file='config.json')[source]¶
- bmtk.utils.sim_setup.build_env_pointnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=-15.0, nsteps_block=5000, v_init=-80.0, celsius=34.0, report_vars=[], report_nodes=None, current_clamp=None, spikes_inputs=None, use_relative_paths=True, config_file=None)[source]¶